MmuINT0141068 @ mm10
Intron Retention
Gene
ENSMUSG00000034684 | Sema3f
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:MGI Symbol;Acc:MGI:1096347]
Coordinates
chr9:107684688-107685547:-
Coord C1 exon
chr9:107685325-107685547
Coord A exon
chr9:107684777-107685324
Coord C2 exon
chr9:107684688-107684776
Length
548 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
TCCTGCCCGGCCCGTTCCAGACC
3' ss Score
6.64
Exon sequences
Seq C1 exon
TGCCCTGGTGGAACCTTCACGCCCTCGATGAAGTCCACTAAGGACTACCCTGATGAAGTGATCAACTTCATGCGCACTCATCCGCTCATGTACCAGGCCGTCTACCCGCTCCAGCGGCGACCCCTGGTGGTCCGTACAGGCGCTCCCTACCGCCTCACCACTGTCGCTGTGGACCAGGTGGATGCAGCTGATGGACGCTATGAGGTGCTTTTCCTGGGCACAG
Seq A exon
GTACCCACTGCTGCTCTCAGACACTCCCACATTGGGCCCACTGGATGGGAGGAGCTGATCCTGAGGCCAGAGCCTGCCCAGCTAGGGGTTGCCCTCCTTGGCCAGAATAGCCAAAGCTAGGAATGGGAAAACTACCATCTCTTTTCCCATTTTGAGGGGCCCACCCTATATCAGGACTTTAAAATAACTTAGGATACAGGGCTCTAACTGTTTGCCCGTATACACACATACACAACGCATGCATGCGTGCTTACTTAAACACACCTTCAAAATCATAGCAACATCCAATTCAGCTGCCCGTTTTCTGTTCTTGGTAGGGCCCAAATTGAGAGTCTGGGTGCAGAGGCAGACCCCGGCTGTGAGCCCCTTTGTCCTGTTCCCGTCCCCCAACAACTCTCCCCTCCGTCCAAGGGAGGTTCTTGAACCTCAGCATGGAAGCCCCGCTCCAATGCCCTAGAGGAGATGGGGCTTTGGTGGGGAAGGGGCTGAGGCTTTGCCCCTTCCCCAGCATCCTCAGCCCCACTGAGGTCCTGCCCGGCCCGTTCCAG
Seq C2 exon
ACCGCGGGACAGTGCAGAAGGTCATCGTGCTGCCCAAGGACGACCAGGAGGTGGAAGAGCTGATGCTAGAGGAAGTGGAGGTCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034684:ENSMUST00000080560:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.160 A=NA C2=0.087
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(16.7=100)
A:
NA
C2:
PF0140314=Sema=FE(6.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCCCTGGTGGAACCTTCA
R:
TGAAGACCTCCACTTCCTCTAGC
Band lengths:
310-858
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types